A couple of months ago the songs transferred from iTunes (I use Windows 7) to my various Apple devices started skipping, scratching when I listened to them. I knew the songs themselves were ok as I could play them fine through iTunes. The symptoms were : songs would skip entire parts, a hissing noise would be heard when the cut occured. The skip would happen at random and would affect some songs but not others. This happened with my iPod nano, my iPod Touch and my iPhone.
At first I thought it was because I stored my library onto my NAS and it somehow became corrupted. So I recreated it. But the problem remained. I wiped out all my devices and retransferred my songs. But the problem remained….
Turned out to be a conflict between ZoneAlarm Extreme Security and iTunes ! As soon as I disabled ZoneAlarm I could transfer the songs and no more hissing/skipping. No need to desinstall ZoneAlarm, just disable it during the transfer and you should be ok. My version of ZoneAlarm Extreme Security is 9.3.037.000.